Unless you use the -in::file::native_exclude_res option, the score application will use the standard Calpha rmsd to the native structure (the one passed to -in:file:native). Then I calcuated the rms between the Ca atoms of smallest structures of the decoy and the native. I fitted the largest structure on its native complex. When I recalculate this rms myself in several programs (pymol, vmd) I find values of 5 A. Rosetta for example calculates rms values of 15 A between a decoy and a native.
VMD MEASURE RMSD FULL
When I look in de full atom score file Rosetta produced, I see rms values that I don't understand. > I tried a pertubation run on two proteins. Apart from that pymol also tends to get rid of some residues which do not align and give RMSD of only those residues which align to some extent. Whatever RMSD you get comes only from the smaller unit of the complex. While in your method, you have superimposed the bigger structure over the native one and the RMSD for that unit will be ~0. Then rotates the decoy to get the best alignment with the native structure. It aligns the whole decoy complex over the native complex by superimposing the center of masses of both the complexes. I think Rosetta calculates the rms of a complex in a different way.
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